Subject: Why should one scale charges down for implicit solvent calculations ?

From: Marc Baaden <[email-masked]>
Date: Tue, 21 May 2002 14:51:59 +0100

Dear colleagues,

I re-iterate my question about charge scaling, as I have received 3
requests for summaries, but no replies.

So if you have any comments on this, or would in any other way like
to contribute (eg stimulate a discussion ?), please do so.

Here is the original question:

I am trying to get hold of a sound reference, providing a rationale
for scaling the charges of ionized groups when doing implicit solvent
calculations (MM, MD, NMA) with eg epsilon=80 or epsilon=f(r).

I am roughly aware of the counterion condensation theory of Manning and
related work, but am not sure whether this is the only argument for
charge scaling.

Scaling factors (for proteins !) that I have seen in the literature seem to
be around eg 0.3. How are they derived (ad hoc ? or by using the Xi=1 relation
of Manning and calculating the charge density of the molecule).

Also Manning's work focused on simple cylindrical models of polyions,
but I am particularly interested in proteins. Is there any work focusing
on this problem ?

Thanks in advance,
  Marc Baaden

-- 
 Dr. Marc Baaden - Laboratory of Molecular Biophysics, Oxford University
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